Hi,
I have 300 FASTA sequences of WGS of ameba. I need to assemble the whole sequence. Are there any tools (webservers or any command-line servers) available to combine the whole genome?
Also Is there any tool to convert FASTA to FASTQ format?
Dear Saad Mughal,
Info below may be helpful:
How to extract/retrieve sequence of genes from whole genome:
researchgate.net›post/How_to_extract…whole_genome
1. download the whole genome from NCBI, for examples, and then finding the name of those genes on the genome database and collect the sequences from corresponding genes shown there? 2. Align all known sequences of the genes, then blast conserved sequences on the whole genome database to find the location of corresponding genes and get their sequences. ... Hii. Can someone tell me is there any tools to retrieve fasta sequence for genes? Cite. Similar questions and discussions.
https://www.researchgate.net/post/How_to_extract_retrieve_sequence_of_genes_from_whole_genome
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Variant calling using command-line tools - Bioinformatics...
melbournebioinformatics.org.au›tutorials…variant…
The command-line scripts are stored in simple bash script format in the scripts directory. For those interested, equivalent slurm scripts to run on Spartan are available in the slurm_scripts directory. Although all tools are installed on the server, we will create a tools directory. Let’s begin by creating a byobu-screen session (see above sections for more help): cd byobu-screen -S workshop. ... There are several files in the reference directory. These included the GATK bundle of reference files downloaded from (ftp://[email protected]/bundle/hg38/). Additional files include in the directory are the BWA index files generated for the reference genome.
https://www.melbournebioinformatics.org.au/tutorials/tutorials/variant_calling_gatk1/variant_calling_gatk1/
How did you get these 300 FASTA sequences? Did you pull it from NCBI or any other database?
If you did sequencing, you should get sequences in FASTQ or BAM format which can then be assembled to get full-length or near full-length contigs.
Convert FASTA to FASTQ format?
The difference between FASTA and FASTQ is that the FASTQ file will have quality scores and sequencing info over each sequence while the FASTA file will just have sequences. So, firstly open your FASTA files and see if they have quality info. If they do, that means they are actually FASTQ files.
Without quality scores, it is not advisable to convert FASTA to FASTQ unless you trust the origin of these sequences. In that case, you can use a dummy score. See
https://www.biostars.org/p/99886/
https://code.google.com/archive/p/fasta-to-fastq/
If you are sure that these 300 sequences form the major part of the genome of your organism of interest, you can do a de-novo assembly with Spades or megahit (not recommended).
OR can map to a reference genome with tools such as BWA and BBMap to generate a mapped genome assembly.
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